specbond.dat

Contents

The default contents of specbond.dat (version 4.5) is as follows:

8
CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
CYS     SG      1       HEM     FE      2       0.25    CYS2    HEME
CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
CYS     SG      1       HEM     CAC     1       0.18    CYS2    HEME
HIS     NE2     1       HEM     FE      1       0.2     HIS1    HEME
MET     SD      1       HEM     FE      1       0.24    MET     HEME
CO      C       1       HEME    FE      1       0.19    CO      HEME
CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2

The nine columns respectively indicate

1. residue name A
2. atom name A
3. number of bonds that this atom can form
4. residue name B
5. atom name B
6. number of bonds that this atom can form
7. the reference length for searching for candidate bonds, the margin is ±10%
8. the new name for residue A
9. the new name for residue B

To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line.

To generate such a bond, you then need to present a structure to pdb2gmx with the residues and atoms named as above, and the two atoms forming the bond within the cutoff listed above. To make this work you have to put all the branches in one [ moleculetype ] with pdb2gmx -merge (in GROMACS 4.0) or some suitable use of pdb2gmx -chainsep (in GROMACS 4.5 and later).

This procedure can also be used to generate branched or circular polymers.